PDCD11

protein-coding

programmed cell death 11, the group of Minor histocompatibility antigens|SSU processome

Gene summary

PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[supplied by OMIM, Oct 2008]

MANE transcript

NM_014976.2

Inheritance

—

ClinVar variants

U:270B:15

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr10:103,396,626-103,446,294

External References & Databases

Ensembl (ENSG00000148843)

Transcript & Mutation Effects

hg38 • Region Span ~49.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDCD11 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 250

not providedTotal: 9

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014976.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	3 clinvar		9
missense			257 clinvar	12 clinvar		269
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	270	15	0	285

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014976.2	RefSeq	NP_055791.1	35	MANE Select
ENST00000369797.8	Ensembl	ENSP00000358812.3	35	MANE Select
NM_001411058.1	RefSeq	NP_001397987.1	35	Standard
NM_001437420.1	RefSeq	NP_001424349.1	35	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

rRNA processing
mRNA processing

Molecular Function

RNA binding
protein binding
transcription factor binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytosol
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369797
Coding exons: 35
Length: 49645
Individuals with no LoFs: 125660
Homozygous LoFs: 0
Heterozygous LoFs: 88
Defined: 125748
p: 0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	943	1.04e+3	0.903	0.0000597	12189
Missense (PolyPhen)		284	318.97	0.89038		3701
Synonymous	1.92	385	436	0.883	0.0000266	3754
Loss of Function	4.79	42	91.4	0.459	0.00000527	1056

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00027	0.00027	rare
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.00030	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA. {ECO:0000269|PubMed:17654514}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.682
RVIS EVS: -0.24
RVIS percentile EVS: 36.18

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.965

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High